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Volumn 5251 LNBI, Issue , 2008, Pages 174-185

A faster algorithm for RNA co-folding

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM SPEEDS; ALIGNMENT PROCESSES; DATA SETS; DYNAMIC PROGRAMMING ALGORITHMS; EXPERIMENTAL ANALYSES; NEW ALGORITHMS; OPTIMALITY; POLYMER FOLDING; SPEED-UP; STRUCTURAL ALIGNMENTS; SUB STRUCTURES; TIME COMPLEXITIES;

EID: 56649106364     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-87361-7_15     Document Type: Conference Paper
Times cited : (25)

References (27)
  • 1
    • 33744820625 scopus 로고    scopus 로고
    • Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change
    • Uzilov, A.V., Keegan, J.M., Mathews, D.H.: Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change. BMC Bioinformatics 7, 173 (2005)
    • (2005) BMC Bioinformatics , vol.7 , pp. 173
    • Uzilov, A.V.1    Keegan, J.M.2    Mathews, D.H.3
  • 3
    • 0036295198 scopus 로고    scopus 로고
    • Dynalign: An algorithm for finding the secondary structure common to two RNA sequences
    • Mathews, D., Turner, D.: Dynalign: An algorithm for finding the secondary structure common to two RNA sequences. Journal of Molecular Biology 317, 191-203 (2002)
    • (2002) Journal of Molecular Biology , vol.317 , pp. 191-203
    • Mathews, D.1    Turner, D.2
  • 4
    • 0022146059 scopus 로고
    • Simultaneous solution of the RNA folding, alignment and protose-quence problems
    • Sankoff, D.: Simultaneous solution of the RNA folding, alignment and protose-quence problems. SIAM Journal on Applied Mathematics 45, 810-825 (1985)
    • (1985) SIAM Journal on Applied Mathematics , vol.45 , pp. 810-825
    • Sankoff, D.1
  • 6
    • 0033765362 scopus 로고    scopus 로고
    • Secondary structure alone is generally not statistically significant for the detection of non-coding RNAs
    • Rivas, E., Eddy, S.R.: Secondary structure alone is generally not statistically significant for the detection of non-coding RNAs. Bioinformatics 16, 583-605 (2000)
    • (2000) Bioinformatics , vol.16 , pp. 583-605
    • Rivas, E.1    Eddy, S.R.2
  • 7
    • 34249699636 scopus 로고    scopus 로고
    • Multiple structural alignment and clustering of RNA sequences
    • Torarinsson, E., Havgaard, J.H., Gorodkin, J.: Multiple structural alignment and clustering of RNA sequences. Bioinformatics 23(8), 926-932 (2007)
    • (2007) Bioinformatics , vol.23 , Issue.8 , pp. 926-932
    • Torarinsson, E.1    Havgaard, J.H.2    Gorodkin, J.3
  • 8
    • 36849111485 scopus 로고
    • Shape of a self-avoiding walk or polymer chain
    • Fisher, M.E.: Shape of a self-avoiding walk or polymer chain. J.Chem. Phys. 44, 616-622 (1966)
    • (1966) J.Chem. Phys , vol.44 , pp. 616-622
    • Fisher, M.E.1
  • 10
    • 34547844102 scopus 로고    scopus 로고
    • Murlet: A practical multiple alignment tool for structural RNA sequences
    • Kiryu, H., Tabei, Y., Kin, T., Asai, K.: Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinformatics 23, 1588-1598 (2007)
    • (2007) Bioinformatics , vol.23 , pp. 1588-1598
    • Kiryu, H.1    Tabei, Y.2    Kin, T.3    Asai, K.4
  • 11
    • 25444433586 scopus 로고    scopus 로고
    • Accelerated probabilistic inference of RNA structure evolution
    • Holmes, I.: Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics 6, 73 (2005)
    • (2005) BMC Bioinformatics , vol.6 , pp. 73
    • Holmes, I.1
  • 14
    • 5044242515 scopus 로고    scopus 로고
    • Alignment of RNA base pairing probability matrices
    • Hofacker, I.L., Bernhart, S., Stadler, P.: Alignment of RNA base pairing probability matrices. Bioinformatics 20, 2222-2227 (2004)
    • (2004) Bioinformatics , vol.20 , pp. 2222-2227
    • Hofacker, I.L.1    Bernhart, S.2    Stadler, P.3
  • 15
    • 16344363338 scopus 로고    scopus 로고
    • Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
    • Havgaard, J.H., Lyngso, R.B., Stormo, G.D., Gorodkin, J.: Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics 21(9), 1815-1824 (2005)
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1815-1824
    • Havgaard, J.H.1    Lyngso, R.B.2    Stormo, G.D.3    Gorodkin, J.4
  • 18
    • 0034351060 scopus 로고    scopus 로고
    • Why is the DNA denaturation transition first order?
    • Kafri, Y., Mukamel, D., Peliti, L.: Why is the DNA denaturation transition first order? Physical Review Letters 85, 4988-4991 (2000)
    • (2000) Physical Review Letters , vol.85 , pp. 4988-4991
    • Kafri, Y.1    Mukamel, D.2    Peliti, L.3
  • 19
    • 2942560804 scopus 로고    scopus 로고
    • Gene regulation by riboswitches
    • Mandai, M., Breaker, R.R.: Gene regulation by riboswitches. Cell 6, 451-463 (2004)
    • (2004) Cell , vol.6 , pp. 451-463
    • Mandai, M.1    Breaker, R.R.2
  • 20
    • 0019082587 scopus 로고
    • Fast algorithm for predicting the secondary structure of single-stranded RNA
    • Nussinov, R., Jacobson, A.B.: Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc. Natl. Acad. Sci. 77(11), 6309-6313 (1980)
    • (1980) Proc. Natl. Acad. Sci , vol.77 , Issue.11 , pp. 6309-6313
    • Nussinov, R.1    Jacobson, A.B.2
  • 21
    • 33749412683 scopus 로고    scopus 로고
    • Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints
    • Dowell, R.D., Eddy, S.: Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics 7, 400 (2006)
    • (2006) BMC Bioinformatics , vol.7 , pp. 400
    • Dowell, R.D.1    Eddy, S.2
  • 22
    • 0347755643 scopus 로고    scopus 로고
    • Griffiths-Jones, S.: The microrna. registry. Nucleic Acids R.esearch 32, D109-D111 (2003)
    • Griffiths-Jones, S.: The microrna. registry. Nucleic Acids R.esearch 32, D109-D111 (2003)
  • 23
    • 4143149651 scopus 로고    scopus 로고
    • Consensus folding of aligned sequences as a new measure for the detection of functional R.NAs by comparative genomics
    • Washietl, S., Hofacker, I.L.: Consensus folding of aligned sequences as a new measure for the detection of functional R.NAs by comparative genomics. Journal of Molecular Biology 342, 19-30 (2004)
    • (2004) Journal of Molecular Biology , vol.342 , pp. 19-30
    • Washietl, S.1    Hofacker, I.L.2
  • 24
    • 34547696651 scopus 로고    scopus 로고
    • Lattice Models of Polymers
    • Cambridge University Press, Cambridge
    • Vanderzande, C.: Lattice Models of Polymers (Cambridge Lecture Notes in Physics 11). Cambridge University Press, Cambridge (1998)
    • (1998) Cambridge Lecture Notes in Physics , vol.11
    • Vanderzande, C.1
  • 25
    • 0006572674 scopus 로고
    • Rapid dynamic programming algorithms for RNA secondary structure
    • Waterman, M.S., Smith, T.F.: Rapid dynamic programming algorithms for RNA secondary structure. Adv. Appl. Math. 7, 455-464 (1986)
    • (1986) Adv. Appl. Math , vol.7 , pp. 455-464
    • Waterman, M.S.1    Smith, T.F.2
  • 27
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker, M., Stiegler, P.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research 9(1), 133-148 (1981)
    • (1981) Nucleic Acids Research , vol.9 , Issue.1 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.